setwd("D:\\animesh\\booksNpapers\\bioconductor")
files <-dir(pattern="spot$")
RG <- read.maimages(files, source="spot")
A <- RG$R
B <- RG$G
dim(A)
dim(B)
sum(A<B)
sum(B<A)
mean(A)
RG$genes <- readGAL()
RG$printer <- getLayout(RG$genes)
imageplot(log2(RG$Rb[,1]), RG$printer)
MA <- normalizeWithinArrays(RG)
plotMA(MA) #a = (log2(r) + log2(g))/2 #m=log2(r) - log2(g)
plotMA(MA[,2])
MA <- normalizeBetweenArrays(MA)
fit <- lmFit(MA, design=c(-1,1,-1,1))
options(digits=3); topTable(fit, n=30, adjust="fdr")
MAraw <- normalizeWithinArrays(RG, method="none")
#source("swirl1.r")








